Summary of Study ST002057

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001302. The data can be accessed directly via it's Project DOI: 10.21228/M8DQ4C This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002057
Study TitleDistinct Human Hepatocyte Lipidomics Profiles for Nonalcoholic Steatohepatitis and In Vitro-Induced Steatosis
Study SummaryNonalcoholic steatohepatitis (NASH) is a severe form of steatotic liver injury that can be caused by a variety of stimuli and has a significant mortality rate. A common technique to induce in vitro steatosis involves culturing primary human hepatocytes (PHH) in a fatty acid-enriched media. This study compared the lipidome of PHH cultured in a fatty acid-enriched media to hepatocytes from patients with NASH and healthy controls to determine whether such culture techniques could generate a hepatocellular lipid profile similar to that observed in NASH patients. LC-MS lipidomics analysis of hepatocytes from patients with NASH revealed increases in the total cellular abundance of glycerolipids, phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols, phosphatidylinositols and phosphatidylserines compared to healthy control hepatocytes. PHH cultured in a fatty acid-enriched environment demonstrated an increase in total lipid abundance, however, changes were limited to glycerolipids; in contrast to NASH hepatocytes, increases in the abundance of phospholipids were not observed.
Institute
Monash Institute of Pharmaceutical Sciences
Last NameKralj
First NameThomas
Address381 Royal Parade
EmailTom.Kralj@monash.edu
Phone+61 3 9902 6000
Submit Date2021-12-08
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-01-25
Release Version1
Thomas Kralj Thomas Kralj
https://dx.doi.org/10.21228/M8DQ4C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001302
Project DOI:doi: 10.21228/M8DQ4C
Project Title:Distinct Human Hepatocyte Lipidomes for Nonalcoholic Steatohepatitis and In Vitro-Induced Steatosis
Project Summary:Nonalcoholic steatohepatitis (NASH) is a severe form of steatotic liver injury that can be caused by a variety of stimuli and has a significant mortality rate. A common technique to induce in vitro steatosis involves culturing primary human hepatocytes (PHH) in a fatty acid-enriched media. This study compared the lipidome of PHH cultured in a fatty acid-enriched media to hepatocytes from patients with NASH and healthy controls to determine whether such culture techniques could generate a hepatocellular lipid profile similar to that observed in NASH patients. LC-MS lipidomics analysis of hepatocytes from patients with NASH revealed increases in the total cellular abundance of glycerolipids, phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols, phosphatidylinositols and phosphatidylserines compared to healthy control hepatocytes. PHH cultured in a fatty acid-enriched environment demonstrated an increase in total lipid abundance, however, changes were limited to glycerolipids; in contrast to NASH hepatocytes, increases in the abundance of phospholipids were not observed.
Institute:Monash Institute of Pharmaceutical Sciences
Last Name:Kralj
First Name:Thomas
Address:381 Royal Parade
Email:Tom.Kralj@monash.edu
Phone:+61 3 99026000

Subject:

Subject ID:SU002139
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA193798SM_OSI_S48FFA Treated
SA193799SM_XVN_S52FFA Treated
SA193800SM_OSI_S47FFA Treated
SA193801SM_OSI_S42FFA Treated
SA193802SM_OSI_S41FFA Treated
SA193803SM_XVN_S53FFA Treated
SA193804SM_OSI_S46FFA Treated
SA193805SM_XVN_S58FFA Treated
SA193806SM_XVN_S64FFA Treated
SA193807SM_JHY_S11FFA Treated
SA193808SM_XVN_S63FFA Treated
SA193809SM_XVN_S60FFA Treated
SA193810SM_OSI_S40FFA Treated
SA193811SM_XVN_S59FFA Treated
SA193812SM_XVN_S54FFA Treated
SA193813SM_JPR_S36FFA Treated
SA193814SM_JHY_S18FFA Treated
SA193815SM_JHY_S4FFA Treated
SA193816SM_JHY_S5FFA Treated
SA193817SM_JHY_S17FFA Treated
SA193818SM_JHY_S16FFA Treated
SA193819SM_JHY_S10FFA Treated
SA193820SM_JHY_S12FFA Treated
SA193821SM_JHY_S6FFA Treated
SA193822SM_JPR_S22FFA Treated
SA193823SM_JPR_S34FFA Treated
SA193824SM_JPR_S35FFA Treated
SA193825SM_JPR_S30FFA Treated
SA193826SM_JPR_S29FFA Treated
SA193827SM_JPR_S23FFA Treated
SA193828SM_JPR_S24FFA Treated
SA193829SM_JPR_S28FFA Treated
SA193830NASH_BXW_L1S1NASH From Patient
SA193831NASH_YNM_L4S40NASH From Patient
SA193832NASH_YNM_L4S39NASH From Patient
SA193833NASH_YNM_L4S37NASH From Patient
SA193834NASH_GWD_L2S13NASH From Patient
SA193835NASH_GWD_L2S12NASH From Patient
SA193836NASH_GWD_L2S11NASH From Patient
SA193837NASH_GWD_L2S14NASH From Patient
SA193838NASH_GWD_L2S15NASH From Patient
SA193839NASH_GWD_L2S17NASH From Patient
SA193840NASH_GWD_L2S16NASH From Patient
SA193841NASH_BXW_L1S9NASH From Patient
SA193842NASH_BXW_L1S8NASH From Patient
SA193843NASH_BXW_L1S3NASH From Patient
SA193844NASH_BXW_L1S2NASH From Patient
SA193845NASH_BXW_L1S10NASH From Patient
SA193846NASH_BXW_L1S4NASH From Patient
SA193847NASH_BXW_L1S5NASH From Patient
SA193848NASH_BXW_L1S7NASH From Patient
SA193849NASH_BXW_L1S6NASH From Patient
SA193850NASH_GWD_L2S18NASH From Patient
SA193851NASH_GWD_L2S19NASH From Patient
SA193852NASH_YNM_L4S31NASH From Patient
SA193853NASH_IWM_L3S30NASH From Patient
SA193854NASH_IWM_L3S29NASH From Patient
SA193855NASH_YNM_L4S33NASH From Patient
SA193856NASH_YNM_L4S34NASH From Patient
SA193857NASH_YNM_L4S36NASH From Patient
SA193858NASH_YNM_L4S35NASH From Patient
SA193859NASH_IWM_L3S28NASH From Patient
SA193860NASH_IWM_L3S27NASH From Patient
SA193861NASH_IWM_L3S22NASH From Patient
SA193862NASH_IWM_L3S21NASH From Patient
SA193863NASH_GWD_L2S20NASH From Patient
SA193864NASH_IWM_L3S23NASH From Patient
SA193865NASH_IWM_L3S24NASH From Patient
SA193866NASH_IWM_L3S26NASH From Patient
SA193867NASH_IWM_L3S25NASH From Patient
SA193868NASH_YNM_L4S38NASH From Patient
SA193869NM_JPR_S25Untreated Control
SA193870NM_JPR_S19Untreated Control
SA193871NM_JHY_S9Untreated Control
SA193872NM_JPR_S20Untreated Control
SA193873NM_JPR_S21Untreated Control
SA193874NM_JPR_S27Untreated Control
SA193875NM_JPR_S26Untreated Control
SA193876NM_JHY_S8Untreated Control
SA193877NM_JHY_S7Untreated Control
SA193878NM_JHY_S13Untreated Control
SA193879NM_JHY_S1Untreated Control
SA193880NM_JHY_S14Untreated Control
SA193881NM_JHY_S15Untreated Control
SA193882NM_JHY_S3Untreated Control
SA193883NM_JHY_S2Untreated Control
SA193884NM_JPR_S31Untreated Control
SA193885NM_JPR_S32Untreated Control
SA193886NM_XVN_S51Untreated Control
SA193887NM_XVN_S50Untreated Control
SA193888NM_XVN_S55Untreated Control
SA193889NM_XVN_S56Untreated Control
SA193890NM_XVN_S61Untreated Control
SA193891NM_XVN_S57Untreated Control
SA193892NM_XVN_S49Untreated Control
SA193893NM_OSI_S45Untreated Control
SA193894NM_OSI_S37Untreated Control
SA193895NM_JPR_S33Untreated Control
SA193896NM_OSI_S38Untreated Control
SA193897NM_OSI_S39Untreated Control
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Collection:

Collection ID:CO002132
Collection Summary:Primary Human Hepatocytes provided by BioIVT. Collected from deceased subjects
Sample Type:Cultured cells

Treatment:

Treatment ID:TR002151
Treatment Summary:NASH hepatocytes were taken from patients with NASH. IVIS Hepatocytes were cultured and treated with fatty acid enriched media
Treatment Compound:Free fatty acids
Cell Growth Config:24-well plate

Sample Preparation:

Sampleprep ID:SP002145
Sampleprep Summary:Lipidomics extraction using C:W:M extraction followed by ButOH:MeOH of residual culture plate. Extractions were dried down, combined, and reconstituted.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003349
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000
Column Ascentis Express C8,(2.7um 100mm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units AU

Chromatography:

Chromatography ID:CH002480
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Ascentis Express C8,(2.7um 100mm)
Column Temperature:40
Flow Rate:0.2 mL/min
Sample Injection:10 uL
Solvent A:60% water/40% isopropanol; 2 mM formic acid; 8 mM ammonium carbonate
Solvent B:98% isopropanol/2% water; 2 mM formic acid; 8 mM ammonium carbonate
Chromatography Type:Reversed phase

MS:

MS ID:MS003118
Analysis ID:AN003349
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The LC-MS raw file conversion was performed using ProteoWizard and XCMS. Mzmatch.R was then used for alignment and filtering of peaks with an intensity cut-off of 100,000, relative standard deviation of less than 0.8, and peak shape noise filter of greater than 0.8. Output was then further processed using IDEOM
Ion Mode:UNSPECIFIED
Ion Spray Voltage:3.5 kV
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